Direct Dynamics Simulations of the 3CH2 + 3O2 Reaction at High Temperature.

Direct dynamics simulations with the M06/6-311++G(d,p) level of theory were performed to study the 3CH2 + 3O2 reaction at 1000 K temperature on the ground state singlet surface. The reaction is complex with formation of many different product channels in highly exothermic reactions. CO, CO2, H2O, OH, H2, O, H, and HCO are the products formed from the reaction. The total simulation rate constant for the reaction at 1000 K is (1.2 ± 0.3) × 10-12 cm3 molecule-1 s-1, while the simulation rate constant at 300 K is (0.96 ± 0.28) × 10-12 cm3 molecule-1 s-1. The simulated product yields show that CO is the dominant product and the CO:CO2 ratio is 5.3:1, in good comparison with the experimental ratio of 4.3:1 at 1000 K. On comparing the product yields for the 300 and 1000 K simulations, we observed that, except for CO and H2O, the yields of the other products at 1000 K are lower at 300 K, showing a negative temperature dependence.

Direct Dynamics Simulations of the Unimolecular Decomposition of the Randomly Excited 1CH2O2 Criegee Intermediate. Comparison with 3CH2 + 3O2 Reaction Dynamics.

The 3CH2 + 3O2 reaction has a quite complex ground state singlet potential energy surface (PES). There are multiple minima and transition states before forming the 10 possible reaction products. A previous direct chemical dynamics simulation at the UM06/6-311++G(d,p) level of theory ( J. Phys. Chem. A 2019, 123, 4360-4369) found that reaction on this PES is predominantly direct without trapping in the potential minima. The first minima 3CH2 + 3O2 encounters is that for the 1CH2O2 Criegee intermediate and statistical theory assumes the reactive system is trapped in this intermediate with a lifetime given by Rice-Ramsperger-Kassel-Marcus (RRKM) theory. In the work presented here, a direct dynamics simulation is performed with the above UM06 theory, with the trajectories initialized in the 1CH2O2 intermediate with a random distribution of vibrational energy as assumed by RRKM theory. There are substantial differences between the dynamics for 1CH2O2 dissociation and 3CH2 + 3O2 reaction. For the former there are four product channels, while for the latter there are seven in agreement with experiment. Product energy partitioning for the two simulations are in overall good agreement for the CO2 + H2 and CO + H2O product channels, but in significant disagreement for the HCO + OH product channel. Though 1CH2O2 is excited randomly in accord with RRKM theory, its dissociation probability is biexponential and not exponential as assumed by RRKM. In addition, the 1CH2O2 dissociation dynamics follow non-intrinsic reaction coordinate (non-IRC) pathways. An important finding is that the nonstatistical dynamics for the 3CH2 + 3O2 reaction give results in agreement with experiment.

Pronounced changes in atomistic mechanisms for the Cl- + CH3I SN2 reaction with increasing collision energy.

In a previous direct dynamics simulation of the Cl- + CH3I → ClCH3 + I- SN2 reaction, predominantly indirect and direct reaction was found at collision energies Erel of 0.20 and 0.39 eV, respectively. For the work presented here, these simulations were extended by studying the reaction dynamics from Erel of 0.15 to 0.40 eV in 0.05 eV intervals. A transition from a predominantly indirect to direct reaction is found for Erel of 0.27-0.28 eV, a finding consistent with experiment. The simulation results corroborate the understanding that in experiments indirect reaction is characterized by small product translational energies and isotropic scattering, while direct reaction has higher translational energies and anisotropic scattering. The traditional statistical theoretical model for the Cl- + CH3I SN2 reaction assumes the Cl--CH3I pre-reaction complex (A) is formed, followed by barrier crossing, and then formation of the ClCH3-I- post-reaction complex (B). This mechanism is seen in the dynamics, but the complete atomistic dynamics are much more complex. Atomistic SN2 mechanisms contain A and B, but other dynamical events consisting of barrier recrossing (br) and the roundabout (Ra), in which the CH3-moiety rotates around the heavy I-atom, are also observed. The two most important mechanisms are only formation of A and Ra + A. The simulation results are compared with simulations and experiments for Cl- + CH3Cl, Cl- + CH3Br, F- + CH3I, and OH- + CH3I.

Direct Dynamics Simulations of the CH2 + O2 Reaction on the Ground- and Excited-State Singlet Surfaces.

In a previous work [ Lakshmanan , S. ; J. Phys. Chem. A 2018 , 122 , 4808 - 4818 ], direct dynamics simulations at the M06/6-311++G(d,p) level of theory were reported for 3CH2 (X3B1) + 3O2 (X3∑g-) reaction on its ground-state singlet potential energy surface (PES) at 300 K. However, further analyses revealed the simulations are unstable for the 3CH2 (X3B1) + 3O2 (X3∑g-) reactants on the ground-state singlet surface and the trajectories reverted to an excited-state singlet surface for the 1CH2 (ã1A1) + 1O2 (b1∑g+) reactants. Thus, the dynamics reported previously are for this excited-state singlet PES. The PESs for the 3CH2 (X3B1) + 3O2 (X3∑g-) and 1CH2 (ã1A1) + 1O2 (b1∑g+) reactants are quite similar, and this provided a means to perform simulations for the 3CH2 (X3B1) + 3O2 (X3∑g-) reactants on the ground-state singlet PES at 300 K, which are reported here. The reaction dynamics are quite complex with seven different reaction pathways and nine different products. A consistent set of product yields have not been determined experimentally, but the simulation yields for the H atom, CO, and CO2 are somewhat lower, higher, and lower respectively, than the recommended values. The yields for the remaining six products agree with experimental values. Product decomposition was included in determining the product yields. The simulation 3CH2 + 3O2 rate constant at 300 K is only 3.4 times smaller than the recommended value, which may be accommodated if the 3CH2 + 3O2 → 1CH2O2 potential energy curve is only 0.75 kcal/mol more attractive at the variational transition state for 3CH2 + 3O2 → 1CH2O2 association. The simulation kinetics and dynamics for the 3CH2 + 3O2 and 1CH2 + 1O2 reactions are quite similar. Their rate constants are statistically the same, an expected result, since their transition states leading to products have energies lower than that of the reactants and the attractive potential energy curves for 3CH2 + 3O2 → 1CH2O2 and 1CH2 + 1O2 → 1CH2O2 are nearly identical. The product yields for the 3CH2 + 3O2 and 1CH2 + 1O2 reactions are also nearly identical, only differing for the CO2 yield. The reaction dynamics on both surfaces are predominantly direct, with negligible trapping in potential energy minima, which may be an important contributor to their nearly identical product yields.

Chemical Dynamics Simulation of Energy Transfer: Propylbenzene Cation and N2 Collisions.

Collisional energy transfer of highly vibrationally excited propylbenzene cation in a N2 bath has been studied with chemical dynamics simulations. In this work, an intermolecular potential of propylbenzene cation interacting with N2 was developed from SCS-MP2/6-311++G** ab initio calculations. Using a particle swarm optimization algorithm, the ab initio results were simultaneously fit to a sum of three two-body potentials, consisting of C a-N, C b-N, and H-N, where C a is carbon on the benzene ring and C b is carbon on the propyl side chain. Using the developed intermolecular potential, classical trajectory calculations were performed with a 100.1 kcal/mol excitation energy at 473 K to compare with experiment. Varying the density of the N2 bath, the single collision limit of propylbenzene cation with the N2 bath was obtained at a density of 20 kg/m3 (28 atm). For the experimental excitation energy and in the single collision limit, the average energy transferred per collision, ⟨Δ Ec⟩, is 1.04 ± 0.04 kcal/mol and in good agreement with the experimental value of 0.82 kcal/mol.

Direct Dynamics Simulations of Fragmentation of a Zn(II)-2Cys-2His Oligopeptide. Comparison with Mass Spectrometry Collision-Induced Dissociation.

Abnormalities in zinc metabolism have been linked to many diseases, including different kinds of cancers and neurological diseases. The present study investigates the fragmentation pathways of a zinc chaperon using a model peptide with the sequence acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7 (analog methanobactin peptide-5, amb5). DFT/M05-2X and B3LYP geometry optimizations of [amb5-3H+Zn(II)]- predicted three lowest energy conformers with different chelating motifs. Direct dynamics simulations, using the PM7 semiempirical electronic structure method, were performed for these conformers, labeled a, b, and c, to obtain their fragmentation pathways at different temperatures in the range 1600-2250 K. The simulation results were compared with negative ion mode mass spectrometry experiments. For conformer a, the number of primary dissociation pathways are 11, 14, 24, 70, and 71 at 1600, 1750, 1875, 2000, and 2250 K, respectively. However, there are only 6, 10, 13, 14, and 19 pathways corresponding to these temperatures that have a probability of 2% or more. For conformer b, there are 67 pathways at 2000 K and 71 pathways at 2250 K. For conformer c, 17 pathways were observed at 2000 K. For conformer a, for two of the most common pathways involving C-C bond dissociation, Arrhenius parameters were calculated. The frequency factors and activation energies are smaller than those for C-C homolytic dissociation in alkanes due to increased stability of the product ions as a result of hydrogen bonding. The activation energies agree with the PM7 barriers for the C-C dissociations. Comparison of the simulation and experimental fragmentation ion yields shows the simulations predict double or triple cleavages of the backbone with Zn(II) retaining its binding sites, whereas the experiment exhibits single cleavages of the backbone accompanied by cleavage of two of the Zn(II) binding sites, resulting in b- and y-type ions.

Direct Dynamics Simulation of the Thermal 3CH2 + 3O2 Reaction. Rate Constant and Product Branching Ratios.

The reaction of 3CH2 with 3O2 is of fundamental importance in combustion, and the reaction is complex as a result of multiple extremely exothermic product channels. In the present study, direct dynamics simulations were performed to study the reaction on both the singlet and triplet potential energy surfaces (PESs). The simulations were performed at the UM06/6-311++G(d,p) level of theory. Trajectories were calculated at a temperature of 300 K, and all reactive trajectories proceeded through the carbonyl oxide Criegee intermediate, CH2OO, on both the singlet and triplet PESs. The triplet surface leads to only one product channel, H2CO + O(3P), while the singlet surface leads to eight product channels with their relative importance as CO + H2O > CO + OH + H ∼ H2CO + O(1D) > HCO + OH ∼ CO2 + H2 ∼ CO + H2 + O(1D) > CO2 + H + H > HCO + O(1D) + H. The reaction on the singlet PES is barrierless, consistent with experiment, and the total rate constant on the singlet surface is (0.93 ± 0.22) × 10-12 cm3 molecule-1 s-1 in comparison to the recommended experimental rate constant of 3.3 × 10-12 cm3 molecule-1 s-1. The simulation product yields for the singlet PES are compared with experiment, and the most significant differences are for H, CO2, and H2O. The reaction on the triplet surface is also barrierless, inconsistent with experiment. A discussion is given of the need for future calculations to address (1) the barrier on the triplet PES for 3CH2 + 3O2 → 3CH2OO, (2) the temperature dependence of the 3CH2 + 3O2 reaction rate constant and product branching ratios, and (3) the possible non-RRKM dynamics of the 1CH2OO Criegee intermediate.

Direct Chemical Dynamics Simulations.

In a direct dynamics simulation, the technologies of chemical dynamics and electronic structure theory are coupled so that the potential energy, gradient, and Hessian required from the simulation are obtained directly from the electronic structure theory. These simulations are extensively used to (1) interpret experimental results and understand the atomic-level dynamics of chemical reactions; (2) illustrate the ability of classical simulations to correctly interpret and predict chemical dynamics when quantum effects are expected to be unimportant; (3) obtain the correct classical dynamics predicted by an electronic structure theory; (4) determine a deeper understanding of when statistical theories are valid for predicting the mechanisms and rates of chemical reactions; and (5) discover new reaction pathways and chemical dynamics. Direct dynamics simulation studies are described for bimolecular SN2 nucleophilic substitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments, and semiclassical vibrational spectra. Also included are discussions of quantum effects, the accuracy of classical chemical dynamics simulation, and the methodology of direct dynamics.

Chemical Dynamics Simulations of Energy Transfer for Propylbenzene Cation and He Collisions.

Intermolecular energy transfer for the vibrationally excited propylbenzene cation (C9H12+) in a helium bath was studied with chemical dynamics simulations. The bond energy bond order relationship and electronic structure calculations were used to develop an intramolecular potential for C9H12+. Spin component scaled MP2/6-311++G** calculations were used to develop an intermolecular potential for He + C9H12+. The He + He intermolecular potential was determined from a previous explicitly correlated Gaussian electronic structure calculation. For the simulations, C9H12+ was prepared with a 100.1 kcal/mol excitation energy to compare with experiment. The average energy transfer from C9H12+, ⟨ΔEc⟩, decreased as C9H12+ was vibrationally relaxed and for the initial excitation energy ⟨ΔEc⟩ = 0.64 kcal/mol. This result agrees well with the experimental ⟨ΔEc⟩ value of 0.51 ± 0.26 kcal/mol for collisions of He with the ethylbenzene cation. The ⟨ΔEc⟩ value found for He + C9H12+ collisions is compared with reported values of ⟨ΔEc⟩ for He colliding with other molecules.

Post-transition state dynamics and product energy partitioning following thermal excitation of the F⋯HCH2CN transition state: Disagreement with experiment.

Born-Oppenheimer direct dynamics simulations were performed to study atomistic details of the F + CH3CN → HF + CH2CN H-atom abstraction reaction. The simulation trajectories were calculated with a combined M06-2X/MP2 algorithm utilizing the 6-311++G** basis set. The experiments were performed at 300 K, and assuming the accuracy of transition state theory (TST), the trajectories were initiated at the F⋯HCH2CN abstraction TS with a 300 K Boltzmann distribution of energy and directed towards products. Recrossing of the TS was negligible, confirming the accuracy of TST. HF formation was rapid, occurring within 0.014 ps of the trajectory initiation. The intrinsic reaction coordinate (IRC) for reaction involves rotation of HF about CH2CN and then trapping in the CH2CN⋯HF post-reaction potential energy well of ∼10 kcal/mol with respect to the HF + CH2CN products. In contrast to this IRC, five different trajectory types were observed: the majority proceeded by direct H-atom transfer and only 11% approximately following the IRC. The HF vibrational and rotational quantum numbers, n and J, were calculated when HF was initially formed and they increase as potential energy is released in forming the HF + CH2CN products. The population of the HF product vibrational states is only in qualitative agreement with experiment, with the simulations showing depressed and enhanced populations of the n = 1 and 2 states as compared to experiment. Simulations with an anharmonic zero-point energy constraint gave product distributions for relative translation, HF rotation, HF vibration, CH2CN rotation, and CH2CN vibration as 5%, 11%, 60%, 7%, and 16%, respectively. In contrast, the experimental energy partitioning percentages to HF rotation and vibration are 6% and 41%. Comparisons are made between the current simulation and those for other F + H-atom abstraction reactions. The simulation product energy partitioning and HF vibrational population for F + CH3CN → HF + CH2CN resemble those for other reactions. A detailed discussion is given of possible origins of the difference between the simulation and experimental energy partitioning dynamics for F + CH3CN → HF + CH2CN. The F + CH3CN reaction also forms the CH3C(F)N intermediate, in which the F-atom adds to the C≡N bond. However, this intermediate and F⋯CH3CN and CH3CN⋯F van der Waals complexes are not expected to affect the F + CH3CN → HF + CH2CN product energy partitioning.

Chemical dynamics simulations of energy transfer, surface-induced dissociation, soft-landing, and reactive-landing in collisions of protonated peptide ions with organic surfaces.

There are two components to the review presented here regarding simulations of collisions of protonated peptide ions peptide-H(+) with organic surfaces. One is a detailed description of the classical trajectory chemical dynamics simulation methodology. Different simulation approaches are used, and identified as MM, QM + MM, and QM/MM dependent on the potential energy surface used to represent the peptide-H(+) + surface collision. The second are representative examples of the information that may be obtained from the simulations regarding energy transfer and peptide-H(+) surface-induced dissociation, soft-landing, and reactive-landing for the peptide-H(+) + surface collisions. Good agreement with experiment is obtained for each of these four collision properties. The simulations provide atomistic interpretations of the peptide-H(+) + surface collision dynamics.

Unimolecular dissociation of peptides: statistical vs. non-statistical fragmentation mechanisms and time scales.

In the present work we have investigated mechanisms of gas phase unimolecular dissociation of a relatively simple dipeptide, the di-proline anion, by means of chemical dynamics simulations, using the PM3 semi-empirical Hamiltonian. In particular, we have considered two activation processes that are representative limits of what occurs in collision induced dissociation experiments: (i) thermal activation, corresponding to several low energy collisions, in which the system is prepared with a microcanonical distribution of energy; (ii) collisional activation where a single shock of hundreds of kcal mol-1 (300 kcal mol-1 in the present case) can transfer sufficient energy to allow dissociation. From these two activation processes we obtained different product abundances, and for one particular fragmentation pathway a clear mechanistic difference for the two activation processes. This mechanism corresponds to the leaving of an OH- group and subsequent formation of water by taking a proton from the remaining molecule. This last reaction is always observed in thermal activation while in collisional activation it is less favoured and the formation of OH- as a final product is observed. More importantly, we show that while in thermal activation unimolecular dissociation follows exponential decay, in collision activation the initial population decays with non-exponential behaviour. Finally, from the thermal activation simulations it was possible to obtain rate constants as a function of temperature that show Arrhenius behaviour. Thus activation energies have also been extracted from these simulations.

Chemical Dynamics Simulations of Intermolecular Energy Transfer: Azulene + N2 Collisions.

Chemical dynamics simulations were performed to investigate collisional energy transfer from highly vibrationally excited azulene (Az*) in a N2 bath. The intermolecular potential between Az and N2, used for the simulations, was determined from MP2/6-31+G* ab initio calculations. Az* is prepared with an 87.5 kcal/mol excitation energy by using quantum microcanonical sampling, including its 95.7 kcal/mol zero-point energy. The average energy of Az* versus time, obtained from the simulations, shows different rates of Az* deactivation depending on the N2 bath density. Using the N2 bath density and Lennard-Jones collision number, the average energy transfer per collision ⟨ΔEc⟩ was obtained for Az* as it is collisionally relaxed. By comparing ⟨ΔEc⟩ versus the bath density, the single collision limiting density was found for energy transfer. The resulting ⟨ΔEc⟩, for an 87.5 kcal/mol excitation energy, is 0.30 ± 0.01 and 0.32 ± 0.01 kcal/mol for harmonic and anharmonic Az potentials, respectively. For comparison, the experimental value is 0.57 ± 0.11 kcal/mol. During Az* relaxation there is no appreciable energy transfer to Az translation and rotation, and the energy transfer is to the N2 bath.

Model Simulations of the Thermal Dissociation of the TIK(H+)2 Tripeptide: Mechanisms and Kinetic Parameters.

Direct dynamics simulations, utilizing the RM1 semiempirical electronic structure theory, were performed to study the thermal dissociation of the doubly protonated tripeptide threonine-isoleucine-lysine ion, TIK(H+)2, for temperatures of 1250-2500 K, corresponding to classical energies of 1778-3556 kJ/mol. The number of different fragmentation pathways increases with increase in temperature. At 1250 K there are only three fragmentation pathways, with one contributing 85% of the fragmentation. In contrast, at 2500 K, there are 61 pathways, and not one dominates. The same ion is often formed via different pathways, and at 2500 K there are only 14 m/z values for the product ions. The backbone and side-chain fragmentations occur by concerted reactions, with simultaneous proton transfer and bond rupture, and also by homolytic bond ruptures without proton transfer. For each temperature the TIK(H+)2 fragmentation probability versus time is exponential, in accord with the Rice-Ramsperger-Kassel-Marcus and transition state theories. Rate constants versus temperature were determined for two proton transfer and two bond rupture pathways. From Arrhenius plots activation energies Ea and A-factors were determined for these pathways. They are 62-78 kJ/mol and (2-3) × 1012 s-1 for the proton transfer pathways and 153-168 kJ/mol and (2-4) × 1014 s-1 for the bond rupture pathways. For the bond rupture pathways, the product cation radicals undergo significant structural changes during the bond rupture as a result of hydrogen bonding, which lowers their entropies and also their Ea and A parameters relative to those for C-C bond rupture pathways in hydrocarbon molecules. The Ea values determined from the simulation Arrhenius plots are in very good agreement with the reaction barriers for the RM1 method used in the simulations. A preliminary simulation of TIK(H+)2 collision-induced dissociation (CID), at a collision energy of 13 eV (1255 kJ/mol), was also performed to compare with the thermal dissociation simulations. Though the energy transferred to TIK(H+)2 in the collisions is substantially less than the energy for the thermal excitations, there is substantial fragmentation as a result of the localized, nonrandom excitation by the collisions. CID results in different fragmentation pathways with a significant amount of short time nonstatistical fragmentation. Backbone fragmentation is less important, and side-chain fragmentation is more important for the CID simulations as compared to the thermal simulations. The thermal simulations provide information regarding the long-time statistical fragmentation.

Energy and temperature dependent dissociation of the Na(+)(benzene)1,2 clusters: importance of anharmonicity.

Chemical dynamics simulations were performed to study the unimolecular dissociation of randomly excited Na(+)(Bz) and Na(+)(Bz)2 clusters; Bz = benzene. The simulations were performed at constant energy, and temperatures in the range of 1200-2200 K relevant to combustion, using an analytic potential energy surface (PES) derived in part from MP2/6-311+G* calculations. The clusters decompose with exponential probabilities, consistent with RRKM unimolecular rate theory. Analyses show that intramolecular vibrational energy redistribution is sufficiently rapid within the clusters that their unimolecular dynamics is intrinsically RRKM. Arrhenius parameters, determined from the simulations of the clusters, are unusual in that Ea is ∼10 kcal/mol lower the Na(+)(Bz) → Na(+) + Bz dissociation energy and the A-factor is approximately two orders-of-magnitude too small. Analyses indicate that temperature dependent anharmonicity is important for the Na(+)(Bz) cluster's unimolecular rate constants k(T). This is consistent with the temperature dependent anharmonicity found for the Na(+)(Bz) cluster from a Monte Carlo calculation based on the analytic PES used for the simulations. Apparently temperature dependent anharmonicity is quite important for unimolecular dissociation of the Na(+)(Bz)1,2 clusters.

Dynamics of energy transfer and soft-landing in collisions of protonated dialanine with perfluorinated self-assembled monolayer surfaces.

Chemical dynamics simulations are reported which provide atomistic details of collisions of protonated dialanine, ala2-H(+), with a perfluorinated octanethiolate self-assembled monolayer (F-SAM) surface. The simulations are performed at collision energies Ei of 5.0, 13.5, 22.5, 30.00, and 70 eV, and incident angles 0° (normal) and 45° (grazing). Excellent agreement with experiment (J. Am. Chem. Soc., 2000, 122, 9703-9714) is found for both the average fraction and distribution of the collision energy transferred to the ala2-H(+) internal degrees of freedom. The dominant pathway for this energy transfer is to ala2-H(+) vibration, but for Ei = 5.0 eV ∼20% of the energy transfer is to ala2-H(+) rotation. Energy transfer to ala2-H(+) rotation decreases with increase in Ei and becomes negligible at high Ei. Three types of collisions are observed in the simulations: i.e. those for which ala2-H(+) (1) directly scatters off the F-SAM surface; (2) sticks/physisorbs on/in the surface, but desorbs within the 10 ps numerical integration of the simulations; and (3) remains trapped (i.e. soft-landed) on/in the surface when the simulations are terminated. Penetration of the F-SAM by ala2-H(+) is important for the latter two types of events. The trapped trajectories are expected to have relatively long residence times on the surface, since a previous molecular dynamics simulation (J. Phys. Chem. B, 2014, 118, 5577-5588) shows that thermally accommodated ala2-H(+) ions have an binding energy with the F-SAM surface of at least ∼15 kcal mol(-1).

Properties of complexes formed by Na(+), Mg(2+), and Fe(2+) binding with benzene molecules.

A theoretical investigation was performed to study cation-π interactions in complexes of benzene (Bz) with cations, that is, M(z+)(Bz)n for M(z+) = Na(+), Mg(2+), Fe(2+) and n = 1-3, using MP2 theory with the 6-31+G* and 6-311++G** basis sets and the DFT/(B3LYP and B3LYP-D)/6-311++G** methods. Binding energies and structures of the complexes are reported. The splitting between the quintet and single states of the Fe(2+) complexes was found to depend on the number of benzene molecules in the complex and the complex's structure. All of the M(z+)(Bz) complexes prefer a half-sandwich geometry. A geometry with the cation sandwiched between the two benzene rings was found for the M(z+)(Bz)2 complexes, with the benzene rings either in an eclipsed or staggered conformation. An approximate cyclic structure, with the cation at its center, was found for three benzene molecules interacting with the cation. The cation-benzene binding energy is substantial and equal to 22, 108, and 151 kcal/mol for the Na(+)(Bz), Mg(2+)(Bz), and Fe(2+)(Bz) complexes, respectively. The strength of the interaction of the cation with an individual benzene molecule decreases as the number of benzene molecules bound to the cation increases; for example, it is 108 kcal/mol for Mg(2+)(Bz), but only 71 kcal/mol for Mg(2+)(Bz)3. There is a range of values for the M(z+)(Bz)n intermolecular vibrational frequencies; for example, they are ∼230-360 and ∼10-330 cm(-1) for the Mg(2+)(Bz) and Mg(2+)(Bz)3 complexes, respectively. Binding of the cation to benzene both red and blue shifts the benzene vibrational frequencies. This shifting is larger for the Mg(2+) and Fe(2+) complexes, as compared to those for Na(+), as a result of the former's stronger cation-benzene binding. The present study is an initial step to understand the possible importance of cation-π interactions for polycyclic aromatic hydrocarbon aggregation processes during soot formation.

A unified model for simulating liquid and gas phase, intermolecular energy transfer: N2 + C6F6 collisions.

Molecular dynamics simulations were used to study relaxation of a vibrationally excited C6F6* molecule in a N2 bath. Ab initio calculations were performed to develop N2-N2 and N2-C6F6 intermolecular potentials for the simulations. Energy transfer from "hot" C6F6 is studied versus the bath density (pressure) and number of bath molecules. For the large bath limit, there is no heating of the bath. As C6F6* is relaxed, the average energy of C6F6* is determined versus time, i.e., ⟨E(t)⟩, and for each bath density ⟨E(t)⟩ is energy dependent and cannot be fit by a single exponential. In the long-time limit C6F6 is fully equilibrated with the bath. For a large bath and low pressures, the simulations are in the fixed temperature, independent collision regime and the simulation results may be compared with gas phase experiments of collisional energy transfer. The derivative d[⟨E(t)⟩]/dt divided by the collision frequency ω of the N2 bath gives the average energy transferred from C6F6* per collision ⟨ΔE(c)⟩, which is in excellent agreement with experiment. For the ~100-300 ps simulations reported here, energy transfer from C6F6* is to N2 rotation and translation in accord with the equipartition model, with no energy transfer to N2 vibration. The energy transfer dynamics from C6F6* is not statistically sensitive to fine details of the N2-C6F6 intermolecular potential. Tests, with simulation ensembles of different sizes, show that a relatively modest ensemble of only 24 trajectories gives statistically meaningful results.

A first principles molecular dynamics study of lithium atom solvation in binary liquid mixture of water and ammonia: structural, electronic, and dynamical properties.

The preferential solvation of solutes in mixed solvent systems is an interesting phenomenon that plays important roles in solubility and kinetics. In the present study, solvation of a lithium atom in aqueous ammonia solution has been investigated from first principles molecular dynamics simulations. Solvation of alkali metal atoms, like lithium, in aqueous and ammonia media is particularly interesting because the alkali metal atoms release their valence electrons in these media so as to produce solvated electrons and metal counterions. In the present work, first principles simulations are performed employing the Car-Parrinello molecular dynamics method. Spontaneous ionization of the Li atom is found to occur in the mixed solvent system. From the radial distribution functions, it is found that the Li(+) ion is preferentially solvated by water and the coordination number is mostly four in its first solvation shell and exchange of water molecules between the first and second solvation shells is essentially negligible in the time scale of our simulations. The Li(+) ion and the unbound electron are well separated and screened by the polar solvent molecules. Also the unbound electron is primarily captured by the hydrogens of water molecules. The diffusion rates of Li(+) ion and water molecules in its first solvation shell are found to be rather slow. In the bulk phase, the diffusion of water is found to be slower than that of ammonia molecules because of strong ammonia-water hydrogen bonds that participate in solvating ammonia molecules in the mixture. The ratio of first and second rank orientational correlation functions deviate from 3, which suggests a deviation from the ideal Debye-type orientational diffusion. It is found that the hydrogen bond lifetimes of ammonia-ammonia pairs is very short. However, ammonia-water H-bonds are found to be quite strong when ammonia acts as an acceptor and these hydrogen bonds are found to live longer than even water-water hydrogen bonds.

A first principles molecular dynamics study of excess electron and lithium atom solvation in water-ammonia mixed clusters: structural, spectral, and dynamical behaviors of [(H2O)5NH3]- and Li(H2O)5NH3 at finite temperature.

First principles molecular dynamics simulations are carried out to investigate the solvation of an excess electron and a lithium atom in mixed water-ammonia cluster (H(2)O)(5)NH(3) at a finite temperature of 150 K. Both [(H(2)O)(5)NH(3)](-) and Li(H(2)O)(5)NH(3) clusters are seen to display substantial hydrogen bond dynamics due to thermal motion leading to many different isomeric structures. Also, the structures of these two clusters are found to be very different from each other and also very different from the corresponding neutral cluster without any excess electron or the metal atom. Spontaneous ionization of Li atom occurs in the case of Li(H(2)O)(5)NH(3). The spatial distribution of the singly occupied molecular orbital shows where and how the excess (or free) electron is primarily localized in these clusters. The populations of single acceptor (A), double acceptor (AA), and free (NIL) type water and ammonia molecules are found to be significantly high. The dangling hydrogens of these type of water or ammonia molecules are found to primarily capture the free electron. It is also found that the free electron binding motifs evolve with time due to thermal fluctuations and the vertical detachment energy of [(H(2)O)(5)NH(3)](-) and vertical ionization energy of Li(H(2)O)(5)NH(3) also change with time along the simulation trajectories. Assignments of the observed peaks in the vibrational power spectra are done and we found a one to one correlation between the time-averaged populations of water and ammonia molecules at different H-bonding sites with the various peaks of power spectra. The frequency-time correlation functions of OH stretch vibrational frequencies of these clusters are also calculated and their decay profiles are analyzed in terms of the dynamics of hydrogen bonded and dangling OH modes. It is found that the hydrogen bond lifetimes in these clusters are almost five to six times longer than that of pure liquid water at room temperature.